time domain and frequency domain

If you can see your NMR spectra on a computer it’s because they are in a digital format. From a computer's point of view, a spectrum is a sequence of numbers. Initially, before you start manipulating them, the points correspond to the magnetization of your sample collected at regular intervals of time. This sequence of points is known, in NMR jargon, as the FID (free induction decay). Most of the tools that enrich iNMR are meant to work in the frequency domain; they are disabled when the spectrum is in time domain. Indeed, the main processing task is to transform the time-domain FID into a frequency-domain spectrum. The operation that performs this task is called Fourier Transform (FT). The algorithm of choice is called Fast Fourier Transform (FFT) and has a characteristic requirement: the number of points in the input FID must be a power of 2. You don’t have to worry about this, because it’s all handled (and supplemented, if necessary) by the computer- but knowing this fact will help you to understand why the size of a spectrum (at least after the FFT) is always a power of 2.
A simple way of recognizing if the spectrum is in the time domain or in the frequency domain is by observing the state of the FT command (first item of the Process menu). If it is enabled, the spectrum is still in time domain.

complex and real

Good quality spectra, i.e. the totality of today's spectra, are collected in two channels, called the real and imaginary components. The names are appropriate because we always see the real part and (almost) never see the imaginary one. A spectrum composed of both parts is said to be complex. Many important operations, like FFT and phase correction, require a complex operand. Other operations, like certain types of baseline correction, require instead a real operand (that is, a single channel). In this case, iNMR transforms the complex spectrum into a real spectrum. As you can guess, this simple operation merely consists in throwing away the imaginary component. You can explicitly perform the same operation with the command Process > Make Real. The name of the command will then become: Make Complex. The inverse operation (from Real to Complex) is more complicated, mathematically speaking (but is all dealt with by iNMR, so you don’t have to worry).
Phase correction is the name of the operation that remixes the real and imaginary components. The corrected real part will contain the absorption mode (symmetrical and narrow) of the signals, while the imaginary part will contain the dispersion mode (anti-symmetrical and wide) of the same signals.

workflow

You can perform many operations on a spectrum, but iNMR sets some limits to your freedom. The order in which the operations are performed by iNMR is pre-established (see list below). You are sometimes allowed to mix and repeat the operations that are written on the same row:

Shuffling, Weighting, Zero-Filling, Fourier Transform.

Baseline Correction, Reference Deconvolution, Noise Reduction, Symmetrization, Binning.

iNMR remembers the parameters you have used and inserts them into its own pre-established workflow. When opening a document, iNMR, in its default configuration, looks for processing parameters saved in the past. When a spectrum is opened with iNMR for the first time, no processing parameters can be found and therefore nothing happens (you see the raw data, alias the FID). Instead, if the parameters are found, iNMR performs the processing in the order stated above. Whenever you want to change a parameter, you need to reload the raw data (using the command File > Reload) and start over. This is not terribly complicated. A single click of the gears icon, for example, can repeat the entire command sequence: Solvent Suppression, Shuffling, Weighting, LP-filling, FFT and Phase Correction.

Learn to use the command Reload, because it is more flexible than the command Undo. The latter invisibly calls Reload and repeats all the processing but the last step. Undo does not revert the processing parameters.

second and third dimension

Many useful NMR experiments have 2 or more time dimensions, called t-1, t-2, etc. The last to appear in the pulse sequence (the one with the highest index) is the dimension directly acquired by the probe. These dimensions are transformed in reverse order. Take a 2-D spectrum for example. It appears as a series of 1-D spectra (rows). The directly acquired dimension, i.e., the traditional dimension, is f-2. After the first FT (along f-2) each row becomes a 1-D spectrum in frequency domain, while each column corresponds to a 1-D FID in time domain.

transposition

Modern computers are optimized to process the rows of a matrix, not the columns. It takes more time to process the columns than to transpose the matrix and process the rows (after transposition the old columns become the new rows). For this practical reason, iNMR always transposes a matrix whenever you ask the program to perform an operation along the columns. When the task is completed, the program ignores which dimension you are going to perform the next operation along, and therefore leaves the matrix transposed. The rationale behind this is that since transposition itself can be lengthy it is only performed when strictly necessary (for a computer program, laziness is often a virtue- this is true of systems that use virtual memory). You can also transpose a matrix manually.

extraction

It is possible to extract a single plane from a 3-D matrix and a single row/column from a 2-D matrix. iNMR duplicates the extracted plane (or vector) and you are free to experiment with it while the original matrix is preserved, remaining stored in the memory, but not visible. It becomes visible again only when you close the extract. While the data points are duplicated and preserved, the processing parameters are shared. When you return to the bigger matrix, its phase is updated according to the new values. If you want to see both the big matrix and the extract at the same time, you need to save the latter as a separate file.

exporting

iNMR only stores the parameters, not the processed data. All the calculations are repeated every time you reopen the spectrum. This usually takes a fraction of a second. For large spectra, should the calculations be very lengthy, you can save the processed data with the command “Export”, which corresponds to “Save a Copy As” in other programs. Why has the name been changed? To discourage the inexperienced user from using this command! Having two versions of the same spectrum is a source of confusion and may lead to the loss of the original data.

custom workflow

iNMR contains a console that can be used like a command line. Most of the operations have an associated literal command. You can combine several commands into a script. In this way you can disregard the pre-established order and invent your own workflow. The scripts can be saved both outside and within a spectrum. It is therefore possible to store and repeat these unorthodox workflows.

Related Topics

FT options

Reducing the Number of Dimensions

Processing index